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In Print: Last Week's Sequencing-Related Papers of Note: Mar 6, 2012


Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach.
Poland JA, Brown PJ, Sorrells ME, Jannink JL.
PLoS One. 2012;7(2):e32253.

Fast gapped-read alignment with Bowtie 2.
Langmead B, Salzberg SL.
Nat Methods. 2012 Mar 4. [Epub ahead of print]

Improving ChIP-seq peak-calling for functional co-regulator binding by integrating multiple sources of biological information.
Osmanbeyoglu HU, Hartmaier RJ, Oesterreich S, Lu X.
BMC Genomics. 2012 Jan 17;13 Suppl 1:S1.

Evaluating characteristics of de novo assembly software on 454 transcriptome data: a simulation approach.
Mundry M, Bornberg-Bauer E, Sammeth M, Feulner PG.
PLoS One. 2012;7(2):e31410.

Assessment of metagenomic assembly using simulated next generation sequencing data.
Mende DR, Waller AS, Sunagawa S, Järvelin AI, et al.
PLoS One. 2012;7(2):e31386.

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
Trapnell C, Roberts A, Goff L, Pertea G, et al.
Nat Protoc. 2012 Mar 1;7(3):562-78.

Combination of de novo assembly of massive sequencing reads with classical repeat prediction improves identification of repetitive sequences in Schistosoma mansoni.
Lepesant JM, Roquis D, Emans R, Cosseau C, et al.
Exp Parasitol. 2012 Feb 21. [Epub ahead of print]

FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads.
Zhang G, Fedyunin I, Kirchner S, Xiao C, et al.
Nucleic Acids Res. 2012 Feb 29. [Epub ahead of print]

All your base: a fast and accurate probabilistic approach to base calling.
Massingham T, Goldman N.
Genome Biol. 2012 Feb 29;13(2):R13.

Identification of long non-protein coding RNAs in chicken skeletal muscle using next generation sequencing.
Li T, Wang S, Wu R, Zhou X, et al.
Genomics. 2012 Feb 20. [Epub ahead of print]

Comparative study of statistical methods for detecting association with rare variants in exome-resequencing data.
Saad M, Pierre AS, Bohossian N, Macé M, Martinez M.
BMC Proc. 2011 Nov 29;5 Suppl 9:S33.

Genome-wide determination of RNA stability reveals hundreds of short-lived non-coding transcripts in mammals.
Tani H, Mizutani R, Salam KA, Tano K, et al.
Genome Res. 2012 Feb 27. [Epub ahead of print]

Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels.
Schulz MH, Zerbino DR, Vingron M, Birney E.
Bioinformatics. 2012 Feb 24. [Epub ahead of print]

Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes.
Hughes JF, Skaletsky H, Brown LG, Pyntikova T, et al.
Nature. 2012 Feb 22;483(7387):82-6.

Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA.
Khil PP, Smagulova F, Brick KM, Camerini-Otero RD, Petukhova GV.
Genome Res. 2012 Feb 24. [Epub ahead of print]

The Basque paradigm: genetic evidence of a maternal continuity in the Franco-Cantabrian region since pre-neolithic times.
Behar DM, Harmant C, Manry J, van Oven M, et al.
Am J Hum Genet. 2012 Feb 21. [Epub ahead of print]

Influence of wet distillers grains diets on beef cattle fecal bacterial community structure.
Rice WC, Galyean ML, Cox SB, Dowd SE, Cole NA.
BMC Microbiol. 2012 Feb 24;12(1):25.

Optimizing a massive parallel sequencing workflow for quantitative miRNA expression analysis.
Cordero F, Beccuti M, Arigoni M, Donatelli S, Calogero RA.
PLoS One. 2012;7(2):e31630.

De novo transcriptome of safflower and the identification of putative genes for oleosin and the biosynthesis of flavonoids.
Li H, Dong Y, Yang J, Liu X, et al.
PLoS One. 2012;7(2):e30987.

5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing.
Takahashi H, Lassmann T, Murata M, Carninci P.
Nat Protoc. 2012 Feb 23;7(3):542-61.

Transcriptome atlases of mouse brain reveals differential expression across brain regions and genetic backgrounds.
Sun W, Lee S, Zhabotynsky V, Zou F, et al.
G3 (Bethesda) . 2012 Feb;2(2):203-11.

Multiplex chromosomal exome sequencing accelerates identification of ENU-induced mutations in the mouse.
Sun M, Mondal K, Patel V, Horner VL, et al.
G3 (Bethesda) . 2012 Jan;2(1):143-50.

Deep-sequencing protocols influence the results obtained in small-RNA sequencing.
Toedling J, Servant N, Ciaudo C, Farinelli L, et al.
PLoS One. 2012;7(2):e32724.

The Scan

Wolf Howl Responses Offer Look at Vocal Behavior-Related Selection in Dogs

In dozens of domestic dogs listening to wolf vocalizations, researchers in Communication Biology see responses varying with age, sex, reproductive status, and a breed's evolutionary distance from wolves.

Facial Imaging-Based Genetic Diagnoses Appears to Get Boost With Three-Dimensional Approach

With data for more than 1,900 individuals affected by a range of genetic conditions, researchers compared facial phenotype-based diagnoses informed by 2D or 3D images in the European Journal of Human Genetics.

Survey Suggests Multigene Cancer Panel VUS Reporting May Vary Across Genetic Counselors

Investigators surveyed dozens of genetic counselors working in clinical or laboratory settings, uncovering attitudes around VUS reporting after multigene cancer panel testing in the Journal of Genetic Counseling.

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.